Over the last century, the development of charged particle microscopes (CPMs) has led to the observation of natural phenomena at magnifications far greater than can be achieved in optical microscopy. The basic electron microscope has evolved into several classes of devices, such as the Transmission Electron Microscope (TEM), Scanning Electron Microscope (SEM), and Scanning Transmission Electron Microscope (STEM), and also into various sub-species, such as so-called “dual-beam” tools (such as a FIB-SEM), which combine a microscope with a “machining” Focused Ion Beam (FIB), allowing supportive activities such as ion-beam milling or Ion-Beam-Induced Deposition (IBID), for example.
In the operation of a SEM, irradiation of a specimen by a scanning electron beam causes emission of “auxiliary” radiation from the specimen, in the form of secondary electrons, backscattered electrons, X-rays and photoluminescence (infrared, visible and/or ultraviolet photons), for example. Such emissions may then be detected, alone or in combination, and accumulated over the course of scanning process to create an image.
As an alternative to using electrons as the irradiating beam, charged-particle microscopes can also use other species of charged particle. In this regard, the phrase “charged particle” should be broadly interpreted as encompassing electrons, positive ions (for example, Ga or He ions), negative ions, protons and positrons.
Typically, a scanning-type CPM microscope will comprise at least the following components:                A radiation source, such as a Schottky electron source or an ion gun        A focusing column of components which manipulate the radiation beam from the source by performing certain operations such as focusing, aberration mitigation, cropping (with an aperture), or filtering. The column will generally include one or more charged-particle lenses, and may comprise other types of particle-optical component also. Often, the column includes a deflector system that uses a field to deflect the output beam to perform a scanning motion across the specimen being investigated.        A specimen holder, on which a specimen or workpiece under investigation is held and positioned (e.g. tilted, rotated). If desired, this holder may also be movable to effect a relative motion of the beam with respect to the specimen to assist in scanning. In general, such a specimen holder will be connected to a positioning system such as a mechanical stage.        A detector, which may be unitary, or compound or distributed in nature, and which can take many different forms depending on the radiation being detected. Examples of electron detectors include scintillator-photomultiplier combinations (referred to “Everhart Thornley” detectors) and solid state detectors, including solid-state photomultipliers, photodiodes, CMOS detectors, and CCD detectors. Photon detectors can detect cathodoluminescence, light emitted as an electron impacts the sample, and x-rays and can include photovoltaic cells, photomultipliers (both tubes and solid state), and other solid state detectors.        
Although various forms of scanning microscopy have been known for decades, scanning-based imaging tends to be a relatively slow and tedious process, and has therefore been limited to investigating very small specimens or portions thereof, for example on a typical scale of tens of nanometers in CPMs and tens of microns in confocal microscopy. Yet, in many technical fields that use CPMs, there is an increasing need to maintain the resolution offered by these techniques, but to expand the imaging areas by orders of magnitude. Further, in recent years, there has been increasing need to adapt SEM technologies for high-throughput applications, such as high-throughput DNA sequencing, high-speed biological sample scanning (examination of tissue), and high-speed analysis of natural resources samples (examination of core samples).
Another problem with present-day scanning microscopy techniques can occur when imaging radiation-sensitive specimens, such as biological specimens, cryogenic specimens, etc. The issue in this case is that the act of irradiating such specimens with an energetic beam (particularly a charged-particle beam) tends to damage the specimen by causing molecular re-arrangement or mutation, thawing, or desiccation. To mitigate this effect, some existing systems reduce the intensity or increase the scan speed of the irradiating beam. However, such measures generally lead to an undesirable decrease in signal-to-noise ratio (SNR).
Further, forming a high resolution digital scan of a 3D volume by a scanning electron microscope (SEM)/focused ion beam (FIB) dual beam device is a useful tool in the fields of biology and natural resource exploitation. In this technique, the FIB repeatedly removes a thin layer of the volume to be imaged, repeatedly exposing surfaces for the SEM to image. The process may collect of an immense amount of data, typically in the giga-pixel range. Such collection is typically a slow process, taking anywhere from 4 to 60 hours, which limits the useful throughput of the device and its usefulness in situations where multiple samples need to be imaged quickly. Scanning a large image field with sparse filling of objects/particles of interest is a therefore rather inefficient process in any of the fields discussed above.